nmr-processing 7.0.1 → 7.3.0

package/lib/assignment/get13CAssignments.d.ts

@@ -1,9 +1,9 @@
 import { Molecule } from 'openchemlib';
 import { NMRRange } from '..';
 import { PredictCarbonOptions } from '../prediction/predictCarbon';
-import { RestrictionByCS } from './utils/buildAssignments';
+import { RestrictionByCS1D } from './utils/buildAssignments';
 export interface Get13CAssignmentsOptions {
-    restrictionByCS?: Partial<RestrictionByCS>;
+    restrictionByCS?: Partial<RestrictionByCS1D>;
     /**
      * min score to accept an assignment
      * @default 1
@@ -30,6 +30,6 @@ export interface Get13CAssignmentsOptions {
     predictionOptions?: PredictCarbonOptions;
 }
 export declare function get13CAssignments(ranges: NMRRange[], molecule: Molecule, options?: Get13CAssignmentsOptions): Promise<{
-    score: any;
+    score: w;
     assignment: unknown[];
 }[]>;

package/lib/assignment/get13CAssignments.js.map

@@ -1 +1 @@
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package/lib/assignment/get1HAssignments.d.ts

@@ -3,11 +3,11 @@ import { NMRRange } from '..';
 import { PredictProtonOptions } from '../prediction/predictProton';
 import type { NMRSignal1D } from '../signals/NMRSignal1D';
 import { MakeMandatory } from '../utilities/MakeMandatory';
-import { RestrictionByCS } from './utils/buildAssignments';
+import { RestrictionByCS1D } from './utils/buildAssignments';
 export declare type NMRSignal1DWithAtomsAndDiaIDs = MakeMandatory<NMRSignal1D, 'atoms' | 'diaIDs' | 'nbAtoms'>;
 export declare type NMRRangeWithIntegration = MakeMandatory<NMRRange, 'integration'>;
 export interface Get1HAssignmentsOptions {
-    restrictionByCS?: Partial<RestrictionByCS>;
+    restrictionByCS?: Partial<RestrictionByCS1D>;
     /**
      * min score to accept an assignment
      * @default 1
@@ -37,6 +37,6 @@ export interface Targets {
     [key: string]: NMRRangeWithIntegration;
 }
 export declare function get1HAssignments(ranges: NMRRange[], molecule: Molecule, options?: Get1HAssignmentsOptions): Promise<{
-    score: any;
+    score: w;
     assignment: unknown[];
 }[]>;

package/lib/assignment/get1HAssignments.js.map

@@ -1 +1 @@
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package/lib/assignment/getAssignments.d.ts

@@ -0,0 +1,81 @@
+import { Molecule } from 'openchemlib';
+import { NMRSignal1D } from '..';
+import type { PredictCarbonOptions } from '../prediction/predictCarbon';
+import type { PredictProtonOptions } from '../prediction/predictProton';
+import { NMRRange } from '../xy/NMRRange';
+import { NMRZone } from '../xyz/NMRZone';
+import { AtomTypes, RestrictionByCS } from './utils/getAssignment/buildAssignments';
+export interface SpectraData1D {
+    id?: string;
+    ranges: NMRRange[];
+    info?: any;
+}
+export interface SpectraData2D {
+    id?: string;
+    zones: NMRZone[];
+    info?: any;
+}
+export declare type SpectraData = SpectraData1D | SpectraData2D;
+export interface GetAutoAssignmentInput {
+    /**
+     * It has the number of each atoms in the chemical structure. e.g. { C: 6, H: 6 }
+     */
+    atoms?: {
+        [key: string]: number;
+    };
+    spectra: SpectraData[];
+    /**
+     * Instance of Molecule
+     */
+    molecule: Molecule;
+}
+export interface GetAssignmentsOptions {
+    justAssign?: Array<AtomTypes[]>;
+    restrictionByCS?: Partial<RestrictionByCS>;
+    /**
+     * min score to accept an assignment
+     * @default 1
+     */
+    minScore?: number;
+    /**
+     * maximal number of assignments to return
+     * @default 10
+     */
+    maxSolutions?: number;
+    /**
+     * number of allowed unassignment signals
+     * @default 0
+     */
+    nbAllowedUnAssigned?: {
+        [key: string]: number;
+    };
+    /**
+     * time limit in miliseconds to finish the assignment procedure.
+     * @default 6000
+     */
+    timeout?: number;
+    /**
+     * predictions
+     */
+    predictions?: {
+        H?: NMRSignal1D[];
+        C?: NMRSignal1D[];
+    };
+    /**
+     * prediction options
+     */
+    predictionOptions?: {
+        H?: PredictProtonOptions;
+        C?: PredictCarbonOptions;
+    };
+    /**
+     * correlation options
+     */
+    correlation?: {
+        tolerance?: number;
+    };
+}
+export declare function getAssignments(input: GetAutoAssignmentInput, options?: GetAssignmentsOptions): Promise<{
+    score: w;
+    assignment: import("./utils/getAssignment/checkIDs").SpectraDataWithIds[];
+}[]>;

package/lib/assignment/getAssignments.js

@@ -0,0 +1,44 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getAssignments = void 0;
+const openchemlib_utils_1 = require("openchemlib-utils");
+const buildAssignments_1 = require("./utils/getAssignment/buildAssignments");
+const checkIDs_1 = require("./utils/getAssignment/checkIDs");
+const getTargetsAndCorrelations_1 = require("./utils/getAssignment/getTargetsAndCorrelations");
+const getWorkFlow_1 = __importDefault(require("./utils/getAssignment/getWorkFlow"));
+async function getAssignments(input, options = {}) {
+    let { restrictionByCS = {}, justAssign, minScore = 1, maxSolutions = 10, nbAllowedUnAssigned, timeout = 6000, predictionOptions = {}, predictions = {}, correlation: correlationOptions = {}, } = options;
+    const { tolerance = { H: 0.2, C: 1 }, useChemicalShiftScore = false, chemicalShiftRestriction = true, } = restrictionByCS;
+    const molecule = input.molecule;
+    if (!molecule)
+        throw new Error('It is needed a molecule to assign');
+    molecule.addImplicitHydrogens();
+    (0, openchemlib_utils_1.addDiastereotopicMissingChirality)(molecule);
+    const spectra = (0, checkIDs_1.checkIDs)(input.spectra);
+    const { targets, correlations } = (0, getTargetsAndCorrelations_1.getTargetsAndCorrelations)(spectra, correlationOptions);
+    const { assignmentOrder } = (0, getWorkFlow_1.default)(correlations, justAssign);
+    const solutions = await (0, buildAssignments_1.buildAssignments)({
+        restrictionByCS: {
+            tolerance,
+            useChemicalShiftScore,
+            chemicalShiftRestriction,
+        },
+        spectra,
+        molecule,
+        timeout,
+        minScore,
+        maxSolutions,
+        assignmentOrder,
+        nbAllowedUnAssigned,
+        correlations,
+        targets,
+        predictionOptions,
+        predictions,
+    });
+    return solutions;
+}
+exports.getAssignments = getAssignments;
+//# sourceMappingURL=getAssignments.js.map

package/lib/assignment/getAssignments.js.map

@@ -0,0 +1 @@
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package/lib/assignment/utils/buildAssignments.d.ts

@@ -1,12 +1,12 @@
 import treeSet from 'ml-tree-set';
 import { Targets, NMRSignal1DWithAtomsAndDiaIDs } from '../get1HAssignments';
-export interface RestrictionByCS {
+export interface RestrictionByCS1D {
     chemicalShiftRestriction: boolean;
     tolerance: number;
     useChemicalShiftScore: boolean;
 }
 export interface BuildAssignmentsProps {
-    restrictionByCS?: Partial<RestrictionByCS>;
+    restrictionByCS?: Partial<RestrictionByCS1D>;
     timeout: number;
     minScore: number;
     useIntegrationRestriction: boolean;
@@ -23,11 +23,11 @@ export interface Signals1DAssignment extends NMRSignal1DWithAtomsAndDiaIDs {
 export interface Predictions1Dassignments {
     [key: string]: Signals1DAssignment;
 }
-export interface StoreAssignments1D {
+export interface StoreAssignments {
     solutions: treeSet;
     nSolutions: number;
 }
 export declare function buildAssignments(props: BuildAssignmentsProps): Promise<{
-    score: any;
+    score: w;
     assignment: unknown[];
 }[]>;

package/lib/assignment/utils/buildAssignments.js.map

@@ -1 +1 @@
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package/lib/assignment/utils/createMapPossibleAssignments.d.ts

@@ -1,7 +1,7 @@
 import { MakeMandatory } from '../../utilities/MakeMandatory';
 import type { Targets } from '../get1HAssignments';
-import type { RestrictionByCS, Predictions1Dassignments } from './buildAssignments';
-declare type RestrictionByCSMandatory = MakeMandatory<RestrictionByCS, 'chemicalShiftRestriction' | 'tolerance' | 'useChemicalShiftScore'>;
+import type { RestrictionByCS1D, Predictions1Dassignments } from './buildAssignments';
+declare type RestrictionByCSMandatory = MakeMandatory<RestrictionByCS1D, 'chemicalShiftRestriction' | 'tolerance' | 'useChemicalShiftScore'>;
 interface CreateMapPossibleAssignments {
     predictions: Predictions1Dassignments;
     restrictionByCS: RestrictionByCSMandatory;

package/lib/assignment/utils/exploreTreeRec.d.ts

@@ -1,9 +1,9 @@
 import type { Targets } from '../get1HAssignments';
-import type { RestrictionByCS, StoreAssignments1D, Predictions1Dassignments } from './buildAssignments';
+import type { RestrictionByCS1D, StoreAssignments, Predictions1Dassignments } from './buildAssignments';
 import type { PossibleAssignmentMap } from './createMapPossibleAssignments';
 export interface ExploreTreeRecProps {
     nSources: number;
-    restrictionByCS: RestrictionByCS;
+    restrictionByCS: RestrictionByCS1D;
     timeout: number;
     timeStart: number;
     maxSolutions: number;
@@ -15,7 +15,7 @@ export interface ExploreTreeRecProps {
     possibleAssignmentMap: PossibleAssignmentMap;
     diaIDPeerPossibleAssignment: string[];
 }
-export declare function exploreTreeRec(props: ExploreTreeRecProps, currentIndex: number, partial: Array<string | null>, store: StoreAssignments1D): StoreAssignments1D | undefined;
+export declare function exploreTreeRec(props: ExploreTreeRecProps, currentIndex: number, partial: Array<string | null>, store: StoreAssignments): StoreAssignments | undefined;
 export interface SolutionAssignment {
     assignment: string[];
     score: number;

package/lib/assignment/utils/exploreTreeRec.js.map

@@ -1 +1 @@
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package/lib/assignment/utils/getAssignment/buildAssignments.d.ts

@@ -0,0 +1,72 @@
+import { Values } from 'nmr-correlation';
+import { Molecule } from 'openchemlib';
+import { NMRSignal1D, PredictCarbonOptions, PredictProtonOptions } from '../../..';
+import { MakeMandatory } from '../../../utilities/MakeMandatory';
+import { SpectraDataWithIds } from './checkIDs';
+import { TargetsByAtomType } from './getTargetsAndCorrelations';
+export declare type AtomTypes = 'H' | 'C';
+export declare type CurrentAtoms = Array<AtomTypes>;
+export interface Partial {
+    [key: string]: Array<string | null>;
+}
+export interface DiaIDPeerPossibleAssignment {
+    [key: string]: string[];
+}
+export interface RestrictionByCS {
+    chemicalShiftRestriction: boolean;
+    tolerance: {
+        [key: string]: number;
+    };
+    useChemicalShiftScore: boolean;
+}
+export interface BuildAssignmentInput {
+    spectra: SpectraDataWithIds[];
+    molecule: Molecule;
+    restrictionByCS: RestrictionByCS;
+    timeout: number;
+    minScore: number;
+    nbAllowedUnAssigned?: {
+        [key: string]: number;
+    };
+    maxSolutions: number;
+    correlations: Values;
+    assignmentOrder: Array<Array<AtomTypes>>;
+    predictions: {
+        H?: NMRSignal1D[];
+        C?: NMRSignal1D[];
+    };
+    predictionOptions: {
+        H?: PredictProtonOptions;
+        C?: PredictCarbonOptions;
+    };
+    targets: TargetsByAtomType;
+}
+declare type NMRSignal1DFromPrediction = MakeMandatory<NMRSignal1D, 'nbAtoms' | 'diaIDs' | 'atoms'>;
+export interface Prediction extends NMRSignal1DFromPrediction {
+    diaIDIndex: number;
+    allHydrogens: number;
+    protonsCount: number;
+    pathLength: number[];
+}
+export interface Predictions {
+    [key: string]: Prediction;
+}
+export interface PredictionsByAtomType {
+    [key: string]: Predictions;
+}
+export interface InfoByAtomType {
+    [key: string]: {
+        nSources: number;
+        currentIndex: number;
+        nbAllowedUnAssigned: number;
+    };
+}
+export declare const getAllHydrogens: {
+    C: (m: Molecule, i: number) => number;
+    H: () => number;
+};
+export declare function buildAssignments(props: BuildAssignmentInput): Promise<{
+    score: w;
+    assignment: SpectraDataWithIds[];
+}[]>;
+export {};

package/lib/assignment/utils/getAssignment/buildAssignments.js

@@ -0,0 +1,205 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.buildAssignments = exports.getAllHydrogens = void 0;
+const ml_tree_set_1 = __importDefault(require("ml-tree-set"));
+const openchemlib_utils_1 = require("openchemlib-utils");
+const predictCarbon_1 = require("../../../prediction/predictCarbon");
+const predictProton_1 = require("../../../prediction/predictProton");
+const createMapPossibleAssignment_1 = require("./createMapPossibleAssignment");
+const exploreTree_1 = require("./exploreTree");
+const isSpectraData1D_1 = require("./isSpectraData1D");
+const searchIndices_1 = require("./searchIndices");
+const comparator = (a, b) => {
+    return b.score - a.score;
+};
+const predictor = { H: predictProton_1.predictProton, C: predictCarbon_1.predictCarbon };
+function checkNMRSignal1D(signals) {
+    const keys = [
+        'nbAtoms',
+        'diaIDs',
+        'atoms',
+    ];
+    for (const signal of signals) {
+        for (let key of keys) {
+            if (!signal[key])
+                throw new Error(`property ${key} does not exist`);
+        }
+    }
+}
+exports.getAllHydrogens = {
+    C: (m, i) => m.getAllHydrogens(i),
+    H: () => 1,
+};
+async function buildAssignments(props) {
+    const { spectra, molecule, restrictionByCS, timeout, minScore, nbAllowedUnAssigned = {}, maxSolutions, correlations, assignmentOrder, predictionOptions, predictions: inputPrediction = {}, targets, } = props;
+    let date = new Date();
+    let timeStart = date.getTime();
+    let lowerBoundScore = minScore;
+    let store = {
+        solutions: new ml_tree_set_1.default(comparator),
+        nSolutions: 0,
+    };
+    const pathLengthMatrix = (0, openchemlib_utils_1.getConnectivityMatrix)(molecule, {
+        pathLength: true,
+    });
+    let infoByAtomType = {};
+    const predictions = {};
+    let possibleAssignmentMap = {};
+    let diaIDPeerPossibleAssignment = {};
+    for (const atomTypesToPredict of assignmentOrder) {
+        for (const atomType of atomTypesToPredict) {
+            const options = predictionOptions[atomType];
+            const predictedSignals = inputPrediction[atomType];
+            let { joinedSignals } = predictedSignals
+                ? { joinedSignals: predictedSignals }
+                : await predictor[atomType](molecule, options);
+            checkNMRSignal1D(joinedSignals);
+            if (!predictions[atomType])
+                predictions[atomType] = {};
+            for (let prediction of joinedSignals) {
+                const diaID = prediction.diaIDs[0];
+                const index = prediction.atoms[0];
+                const allHydrogens = exports.getAllHydrogens[atomType](molecule, index);
+                predictions[atomType][diaID] = {
+                    ...prediction,
+                    diaIDIndex: index,
+                    allHydrogens: prediction.nbAtoms * allHydrogens,
+                    protonsCount: allHydrogens,
+                    pathLength: pathLengthMatrix[index],
+                };
+            }
+            infoByAtomType[atomType] = {
+                nSources: joinedSignals.length,
+                currentIndex: 0,
+                nbAllowedUnAssigned: nbAllowedUnAssigned[atomType] || 0,
+            };
+        }
+        possibleAssignmentMap = (0, createMapPossibleAssignment_1.createMapPossibleAssignment)(possibleAssignmentMap, {
+            restrictionByCS,
+            predictions,
+            targets,
+        });
+        diaIDPeerPossibleAssignment = {};
+        for (const atomType in possibleAssignmentMap) {
+            diaIDPeerPossibleAssignment[atomType] = Object.keys(possibleAssignmentMap[atomType]);
+        }
+        let sourceOfPartials = getSourceOfPartials(store, infoByAtomType, atomTypesToPredict);
+        store = {
+            solutions: new ml_tree_set_1.default(comparator),
+            nSolutions: 0,
+        };
+        for (let partial of sourceOfPartials) {
+            (0, exploreTree_1.exploreTree)({
+                currentAtomTypes: atomTypesToPredict,
+                restrictionByCS,
+                timeout,
+                timeStart,
+                targets,
+                predictions,
+                correlations,
+                maxSolutions,
+                lowerBoundScore,
+                possibleAssignmentMap,
+                diaIDPeerPossibleAssignment,
+            }, infoByAtomType, partial, store);
+        }
+    }
+    return annotateSpectraData({
+        store,
+        spectra,
+        diaIDPeerPossibleAssignment,
+        targets,
+    });
+}
+exports.buildAssignments = buildAssignments;
+function annotateSpectraData(input) {
+    var _a;
+    const { store, spectra, diaIDPeerPossibleAssignment, targets } = input;
+    const { solutions } = store;
+    const mapSignalId = {};
+    const atomTypes = Object.keys(targets);
+    for (const atomType of atomTypes) {
+        const targetByAtomType = targets[atomType];
+        for (const targetId in targetByAtomType) {
+            let target = targetByAtomType[targetId];
+            for (const link of target.link) {
+                const signalId = link.signal.id;
+                if (mapSignalId[signalId])
+                    continue;
+                mapSignalId[link.signal.id] = (0, searchIndices_1.searchIndices)(signalId, spectra);
+            }
+        }
+    }
+    const result = [];
+    for (let solution of solutions.elements) {
+        const spectraResult = JSON.parse(JSON.stringify(spectra));
+        const { assignment, score } = solution;
+        const atomTypes = Object.keys(assignment);
+        for (const atomType of atomTypes) {
+            const targetByAtomType = targets[atomType];
+            const assignmentPeerAtomType = assignment[atomType];
+            for (let index = 0; index < assignmentPeerAtomType.length; index++) {
+                const targetID = assignmentPeerAtomType[index];
+                if (targetID === '*' || !targetID)
+                    continue;
+                const target = targetByAtomType[targetID];
+                const diaId = diaIDPeerPossibleAssignment[atomType][index];
+                for (let link of target.link) {
+                    const { spectrumIndex, elementIndex, signalIndex } = mapSignalId[link.signal.id];
+                    const spectrum = spectraResult[spectrumIndex];
+                    if ((0, isSpectraData1D_1.isSpectraData1D)(spectrum)) {
+                        let { ranges } = spectrum;
+                        let range = ranges[elementIndex];
+                        let signal = range.signals[signalIndex];
+                        if (!signal.diaIDs)
+                            signal.diaIDs = [];
+                        signal.diaIDs.push(diaId);
+                    }
+                    else {
+                        const axis = link.axis;
+                        const signal = spectrum.zones[elementIndex].signals[signalIndex];
+                        if (!signal[axis].diaIDs)
+                            signal[axis].diaIDs = [];
+                        (_a = signal[axis].diaIDs) === null || _a === void 0 ? void 0 : _a.push(diaId);
+                    }
+                }
+            }
+        }
+        result.push({
+            score,
+            assignment: spectraResult,
+        });
+    }
+    return result;
+}
+function getSourceOfPartials(store, infoByAtomType, currentAtoms) {
+    return store.nSolutions > 0
+        ? store.solutions.elements.map((e) => {
+            let currentAssignment = e.assignment;
+            for (const atom of currentAtoms) {
+                currentAssignment[atom] = fillPartial(infoByAtomType[atom].nSources);
+            }
+            return currentAssignment;
+        })
+        : initializePartials(infoByAtomType, currentAtoms);
+}
+function initializePartials(infoByAtomType, currentAtoms) {
+    const partial = {};
+    const atomsType = Object.keys(infoByAtomType);
+    for (const atom of atomsType) {
+        const value = currentAtoms.includes(atom) ? null : '*';
+        partial[atom] = fillPartial(infoByAtomType[atom].nSources, value);
+    }
+    return [partial];
+}
+function fillPartial(nSources, value = null) {
+    const partial = new Array(nSources);
+    for (let i = 0; i < nSources; i++) {
+        partial[i] = value;
+    }
+    return partial;
+}
+//# sourceMappingURL=buildAssignments.js.map

package/lib/assignment/utils/getAssignment/buildAssignments.js.map

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package/lib/assignment/utils/getAssignment/checkIDs.d.ts

@@ -0,0 +1,23 @@
+import type { NMRRange, NMRSignal1D, NMRSignal2D, NMRZone } from '../../..';
+import { MakeMandatory } from '../../../utilities/MakeMandatory';
+import type { SpectraData, SpectraData1D, SpectraData2D } from '../../getAssignments';
+export declare type NMRSignal1DWithId = MakeMandatory<NMRSignal1D, 'id'>;
+export declare type NMRSignal2DWithId = MakeMandatory<NMRSignal2D, 'id'>;
+export interface NMRZoneWithIds extends Omit<NMRZone, 'signals' | 'id'> {
+    id: string;
+    signals: Array<NMRSignal2DWithId>;
+}
+export interface NMRRangeWithIds extends Omit<NMRRange, 'id' | 'signals'> {
+    id: string;
+    signals: Array<NMRSignal1DWithId>;
+}
+export interface SpectraData1DWithIds extends Omit<SpectraData1D, 'ranges'> {
+    ranges: NMRRangeWithIds[];
+}
+export interface SpectraData2DWithIds extends Omit<SpectraData2D, 'zones'> {
+    zones: NMRZoneWithIds[];
+}
+export declare type SpectraDataWithIds = SpectraData1DWithIds | SpectraData2DWithIds;
+export declare function checkIDs(input?: SpectraData[]): SpectraDataWithIds[];
+export declare function hasIDs(data: NMRRange[] | NMRZone[]): asserts data is NMRRangeWithIds[] | NMRZoneWithIds[];
+export declare function addIDs(data: NMRRange[] | NMRZone[]): NMRRangeWithIds[] | NMRZoneWithIds[];